@menu
* Tutorial Introduction::
* Step 1 - Creating the XML Database::
* Step 2 - Building the consensus map::
* Step 3 - Projection of the QTL::
* Step 4 - QTL Clustering::
* Step 5 - Post processing::
@end menu

@node Tutorial Introduction
@section Tutorial Introduction

The input files of the tutorial can be downloaded from the @b{MetaQTL} home page.
In the following sections we assume that you have correctly installed the @b{MetaQTL} jar archive and that you unzip the tutorial archive into the directory @file{data} into the current directory.
Thus, in the @file{data} directory there are the following files:
@itemize @bullet
@item experiments.csv : the mapping experiment table
@item trait_ontology.csv : the trait ontology table
@item marker_dictionary.csv : the marker dictionary table
@item genetic-map : a folder which contains the raw genetic maps of the mapping experiments
@item qtl-map : a folder which contains the result of the QTL detection for each mapping experiment
@item ref-map : a folder which contains the reference map Genetic_2005 from MaizeGDB
@end itemize

@node Step 1 - Creating the XML Database
@section Step 1 - Creating the XML Database
@include tutorial_step1.texi

@node Step 2 - Building the consensus map
@section Step 2 - Building the consensus map
@include tutorial_step2.texi

@node Step 3 - Projection of the QTL
@section Step 3 - Projection of the QTL
@include tutorial_step3.texi

@node Step 4 - QTL Clustering
@section Step 4 - QTL Clustering
@include tutorial_step4.texi

@node Step 5 - Post processing
@section Step 4 - Post processing
@include tutorial_step5.texi
